Starting phenix.real_space_refine on Sun Jul 5 19:25:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b90_44364/07_2026/9b90_44364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b90_44364/07_2026/9b90_44364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b90_44364/07_2026/9b90_44364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b90_44364/07_2026/9b90_44364.map" model { file = "/net/cci-nas-00/data/ceres_data/9b90_44364/07_2026/9b90_44364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b90_44364/07_2026/9b90_44364.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 12 5.49 5 S 152 5.16 5 C 19220 2.51 5 N 5228 2.21 5 O 5100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7397 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 42, 'TRANS': 939} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 18, 'TRP:plan': 1, 'GLN:plan1': 5, 'ARG:plan': 17, 'ASP:plan': 19, 'HIS:plan': 3, 'PHE:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 298 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 9.41, per 1000 atoms: 0.32 Number of scatterers: 29720 At special positions: 0 Unit cell: (169.74, 169.74, 152.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 152 16.00 P 12 15.00 O 5100 8.00 N 5228 7.00 C 19220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.89 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.89 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.89 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.88 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 16 sheets defined 68.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 645 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.646A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 973 Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1176 Processing helix chain 'A' and resid 1177 through 1177 No H-bonds generated for 'chain 'A' and resid 1177 through 1177' Processing helix chain 'B' and resid 7 through 8 No H-bonds generated for 'chain 'B' and resid 7 through 8' Processing helix chain 'B' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.606A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 421 through 436 removed outlier: 4.142A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.649A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 603 Processing helix chain 'B' and resid 607 through 634 Processing helix chain 'B' and resid 634 through 645 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 862 removed outlier: 3.645A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 906 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 916 through 926 Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 973 Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1176 Processing helix chain 'B' and resid 1177 through 1177 No H-bonds generated for 'chain 'B' and resid 1177 through 1177' Processing helix chain 'C' and resid 7 through 8 No H-bonds generated for 'chain 'C' and resid 7 through 8' Processing helix chain 'C' and resid 9 through 15 removed outlier: 4.167A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.723A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.982A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 603 Processing helix chain 'C' and resid 607 through 634 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 862 removed outlier: 3.646A pdb=" N ASP C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 906 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 916 through 926 Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 973 Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.767A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1088 removed outlier: 4.130A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C1082 " --> pdb=" O PRO C1078 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1176 Processing helix chain 'C' and resid 1177 through 1177 No H-bonds generated for 'chain 'C' and resid 1177 through 1177' Processing helix chain 'D' and resid 7 through 8 No H-bonds generated for 'chain 'D' and resid 7 through 8' Processing helix chain 'D' and resid 9 through 15 removed outlier: 4.168A pdb=" N LYS D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.885A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.724A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.607A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.983A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 removed outlier: 3.613A pdb=" N GLY D 386 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 421 through 436 removed outlier: 4.143A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.648A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 603 Processing helix chain 'D' and resid 607 through 634 Processing helix chain 'D' and resid 634 through 645 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 862 removed outlier: 3.646A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 906 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 973 Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.768A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1071 removed outlier: 4.910A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1088 removed outlier: 4.129A pdb=" N VAL D1081 " --> pdb=" O PRO D1077 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE D1082 " --> pdb=" O PRO D1078 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1176 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 7.998A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A 156 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE A 269 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR B 211 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY B 156 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE B 269 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'C' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR C 211 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY C 156 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 261 through 262 removed outlier: 3.956A pdb=" N ILE C 269 " --> pdb=" O THR C 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.173A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'D' and resid 210 through 211 removed outlier: 7.999A pdb=" N TYR D 211 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLY D 156 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 261 through 262 removed outlier: 3.955A pdb=" N ILE D 269 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1936 hydrogen bonds defined for protein. 5616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9608 1.34 - 1.46: 7133 1.46 - 1.58: 13403 1.58 - 1.69: 20 1.69 - 1.81: 228 Bond restraints: 30392 Sorted by residual: bond pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 1.541 1.529 0.012 1.20e-02 6.94e+03 1.04e+00 bond pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 9.06e-01 bond pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 8.62e-01 bond pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 1.541 1.530 0.011 1.20e-02 6.94e+03 8.38e-01 bond pdb=" CB TRP C1124 " pdb=" CG TRP C1124 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.57e-01 ... (remaining 30387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 40631 1.29 - 2.57: 537 2.57 - 3.86: 148 3.86 - 5.15: 48 5.15 - 6.43: 20 Bond angle restraints: 41384 Sorted by residual: angle pdb=" N GLU A 371 " pdb=" CA GLU A 371 " pdb=" CB GLU A 371 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N GLU C 371 " pdb=" CA GLU C 371 " pdb=" CB GLU C 371 " ideal model delta sigma weight residual 114.17 110.49 3.68 1.14e+00 7.69e-01 1.04e+01 angle pdb=" N GLU B 371 " pdb=" CA GLU B 371 " pdb=" CB GLU B 371 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N GLU D 371 " pdb=" CA GLU D 371 " pdb=" CB GLU D 371 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" C3' ATP D2003 " pdb=" C4' ATP D2003 " pdb=" C5' ATP D2003 " ideal model delta sigma weight residual 115.19 111.00 4.19 1.76e+00 3.23e-01 5.66e+00 ... (remaining 41379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 17023 16.76 - 33.51: 665 33.51 - 50.27: 152 50.27 - 67.03: 40 67.03 - 83.79: 20 Dihedral angle restraints: 17900 sinusoidal: 6628 harmonic: 11272 Sorted by residual: dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N PRO B 208 " pdb=" CA PRO B 208 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 17897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4395 0.059 - 0.118: 361 0.118 - 0.177: 20 0.177 - 0.236: 0 0.236 - 0.294: 12 Chirality restraints: 4788 Sorted by residual: chirality pdb=" C2' ATP B2003 " pdb=" C1' ATP B2003 " pdb=" C3' ATP B2003 " pdb=" O2' ATP B2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP A2003 " pdb=" C1' ATP A2003 " pdb=" C3' ATP A2003 " pdb=" O2' ATP A2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP D2003 " pdb=" C1' ATP D2003 " pdb=" C3' ATP D2003 " pdb=" O2' ATP D2003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4785 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 437 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 438 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 437 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO B 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 437 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 438 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 438 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 438 " 0.018 5.00e-02 4.00e+02 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 851 2.70 - 3.25: 34325 3.25 - 3.80: 50589 3.80 - 4.35: 58847 4.35 - 4.90: 99939 Nonbonded interactions: 244551 Sorted by model distance: nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.154 3.250 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.154 3.250 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.154 3.250 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.154 3.250 nonbonded pdb=" OE1 GLN C 831 " pdb="CA CA C2001 " model vdw 2.184 3.250 ... (remaining 244546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.770 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.855 30396 Z= 0.523 Angle : 0.554 28.602 41392 Z= 0.291 Chirality : 0.035 0.294 4788 Planarity : 0.003 0.031 5196 Dihedral : 10.679 83.785 10592 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.42 % Allowed : 5.61 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.14), residues: 3848 helix: 1.66 (0.10), residues: 2440 sheet: -1.03 (0.35), residues: 244 loop : 0.01 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 140 TYR 0.005 0.001 TYR B 968 PHE 0.006 0.001 PHE B1069 TRP 0.006 0.001 TRP C 776 HIS 0.002 0.001 HIS D1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (30392) covalent geometry : angle 0.46791 / 0.25 (41384) SS BOND : bond 0.85409 / 42.78 ( 4) SS BOND : angle 21.29922 / 10.98 ( 8) hydrogen bonds : bond 0.19497 / 13.68 ( 1936) hydrogen bonds : angle 7.37161 / 5.40 ( 5616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 274 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1034 LEU cc_start: 0.9170 (mp) cc_final: 0.8893 (tp) REVERT: B 1034 LEU cc_start: 0.9136 (mp) cc_final: 0.8831 (tp) REVERT: C 1034 LEU cc_start: 0.9099 (mp) cc_final: 0.8819 (tp) REVERT: D 1034 LEU cc_start: 0.9151 (mp) cc_final: 0.8863 (tp) outliers start: 12 outliers final: 8 residues processed: 286 average time/residue: 0.1954 time to fit residues: 90.6059 Evaluate side-chains 205 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN A1037 ASN B 165 HIS B 410 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 GLN C 165 HIS C 410 GLN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 GLN D 410 GLN D 505 HIS D 973 GLN D1037 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.074174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054907 restraints weight = 139633.931| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.87 r_work: 0.2699 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30396 Z= 0.192 Angle : 0.588 10.436 41392 Z= 0.299 Chirality : 0.038 0.160 4788 Planarity : 0.004 0.041 5196 Dihedral : 7.552 86.413 4368 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.64 % Allowed : 8.04 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.14), residues: 3848 helix: 2.59 (0.10), residues: 2476 sheet: -1.02 (0.37), residues: 244 loop : 0.22 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1138 TYR 0.008 0.001 TYR D 227 PHE 0.019 0.001 PHE B 373 TRP 0.011 0.001 TRP A1058 HIS 0.006 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (30392) covalent geometry : angle 0.58754 / 0.30 (41384) SS BOND : bond 0.00240 / 0.12 ( 4) SS BOND : angle 2.46950 / 1.27 ( 8) hydrogen bonds : bond 0.04635 / 3.25 ( 1936) hydrogen bonds : angle 4.87140 / 3.52 ( 5616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.9390 (tpp) cc_final: 0.8753 (mmm) REVERT: A 599 MET cc_start: 0.9132 (ttm) cc_final: 0.8761 (ttm) REVERT: A 669 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 930 VAL cc_start: 0.9254 (t) cc_final: 0.9001 (p) REVERT: A 1034 LEU cc_start: 0.9321 (mp) cc_final: 0.9037 (tp) REVERT: B 477 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9269 (mm) REVERT: B 576 MET cc_start: 0.9200 (mmm) cc_final: 0.8818 (mmm) REVERT: B 599 MET cc_start: 0.9118 (ttm) cc_final: 0.8905 (ttm) REVERT: B 669 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8295 (tm-30) REVERT: B 951 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9314 (mp) REVERT: B 1034 LEU cc_start: 0.9273 (mp) cc_final: 0.8977 (tp) REVERT: B 1146 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8841 (mp0) REVERT: C 430 MET cc_start: 0.9662 (tpp) cc_final: 0.9251 (mmm) REVERT: C 477 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9269 (mm) REVERT: C 576 MET cc_start: 0.9171 (mmm) cc_final: 0.8784 (mmm) REVERT: C 660 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.9072 (mt0) REVERT: C 669 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 951 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9298 (mp) REVERT: C 1034 LEU cc_start: 0.9277 (mp) cc_final: 0.9001 (tp) REVERT: C 1146 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8801 (mp0) REVERT: D 175 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.9281 (mtp) REVERT: D 430 MET cc_start: 0.9635 (tpp) cc_final: 0.9213 (mmm) REVERT: D 477 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9256 (mm) REVERT: D 576 MET cc_start: 0.9229 (mmm) cc_final: 0.8916 (mmm) REVERT: D 669 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8274 (tm-30) REVERT: D 951 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9304 (mp) REVERT: D 1034 LEU cc_start: 0.9319 (mp) cc_final: 0.9005 (tp) REVERT: D 1146 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8769 (mp0) outliers start: 47 outliers final: 14 residues processed: 278 average time/residue: 0.1731 time to fit residues: 79.9892 Evaluate side-chains 228 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 180 optimal weight: 20.0000 chunk 272 optimal weight: 0.6980 chunk 377 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 6 optimal weight: 40.0000 chunk 65 optimal weight: 0.3980 chunk 303 optimal weight: 6.9990 chunk 30 optimal weight: 50.0000 chunk 148 optimal weight: 9.9990 chunk 348 optimal weight: 9.9990 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN B 165 HIS B 410 GLN C 165 HIS C 410 GLN D 410 GLN D 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.074031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.054725 restraints weight = 140358.275| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.86 r_work: 0.2694 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30396 Z= 0.200 Angle : 0.559 9.162 41392 Z= 0.285 Chirality : 0.037 0.160 4788 Planarity : 0.004 0.047 5196 Dihedral : 7.113 86.753 4364 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.78 % Allowed : 9.64 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.14), residues: 3848 helix: 2.52 (0.10), residues: 2484 sheet: -1.04 (0.37), residues: 244 loop : 0.19 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1138 TYR 0.007 0.001 TYR D 227 PHE 0.013 0.001 PHE D 627 TRP 0.010 0.001 TRP D 680 HIS 0.016 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (30392) covalent geometry : angle 0.55919 / 0.28 (41384) SS BOND : bond 0.00506 / 0.25 ( 4) SS BOND : angle 1.31934 / 0.67 ( 8) hydrogen bonds : bond 0.04042 / 2.83 ( 1936) hydrogen bonds : angle 4.64889 / 3.36 ( 5616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.9578 (tpp) cc_final: 0.9113 (mmm) REVERT: A 576 MET cc_start: 0.9367 (tpp) cc_final: 0.8938 (mmm) REVERT: A 599 MET cc_start: 0.9139 (ttm) cc_final: 0.8841 (ttm) REVERT: A 622 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8877 (ttm) REVERT: A 930 VAL cc_start: 0.9208 (t) cc_final: 0.8950 (p) REVERT: A 951 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9293 (mp) REVERT: A 1034 LEU cc_start: 0.9325 (mp) cc_final: 0.9013 (tp) REVERT: A 1125 GLU cc_start: 0.9371 (tt0) cc_final: 0.9159 (tm-30) REVERT: B 430 MET cc_start: 0.9606 (tpp) cc_final: 0.9028 (mmm) REVERT: B 477 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9251 (mm) REVERT: B 576 MET cc_start: 0.9227 (mmm) cc_final: 0.8761 (mmm) REVERT: B 599 MET cc_start: 0.9151 (ttm) cc_final: 0.8692 (ttm) REVERT: B 669 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 951 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9312 (mp) REVERT: B 1034 LEU cc_start: 0.9217 (mp) cc_final: 0.8917 (tp) REVERT: B 1146 GLU cc_start: 0.9440 (mm-30) cc_final: 0.8949 (mp0) REVERT: C 175 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9293 (mtp) REVERT: C 477 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9269 (mm) REVERT: C 576 MET cc_start: 0.9310 (mmm) cc_final: 0.8886 (mmm) REVERT: C 580 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8942 (mt-10) REVERT: C 599 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8835 (ttm) REVERT: C 660 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.9079 (mt0) REVERT: C 669 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 951 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9330 (mp) REVERT: C 1034 LEU cc_start: 0.9228 (mp) cc_final: 0.8951 (tp) REVERT: C 1125 GLU cc_start: 0.9392 (tt0) cc_final: 0.9171 (tt0) REVERT: C 1146 GLU cc_start: 0.9478 (mm-30) cc_final: 0.8956 (mp0) REVERT: D 477 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9261 (mm) REVERT: D 576 MET cc_start: 0.9255 (mmm) cc_final: 0.8916 (mmm) REVERT: D 580 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8867 (mt-10) REVERT: D 599 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8449 (ttp) REVERT: D 951 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9318 (mp) REVERT: D 1034 LEU cc_start: 0.9324 (mp) cc_final: 0.8962 (tp) REVERT: D 1146 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8866 (mp0) outliers start: 51 outliers final: 21 residues processed: 270 average time/residue: 0.1743 time to fit residues: 78.9877 Evaluate side-chains 240 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 113 optimal weight: 7.9990 chunk 198 optimal weight: 0.5980 chunk 386 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 380 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.073416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.053987 restraints weight = 139662.250| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.88 r_work: 0.2670 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30396 Z= 0.248 Angle : 0.582 9.636 41392 Z= 0.294 Chirality : 0.037 0.160 4788 Planarity : 0.004 0.052 5196 Dihedral : 6.988 89.187 4364 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.51 % Allowed : 10.55 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.14), residues: 3848 helix: 2.49 (0.10), residues: 2492 sheet: -1.10 (0.36), residues: 252 loop : 0.15 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 334 TYR 0.008 0.001 TYR D1063 PHE 0.013 0.001 PHE D 627 TRP 0.010 0.001 TRP D 680 HIS 0.007 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (30392) covalent geometry : angle 0.58155 / 0.29 (41384) SS BOND : bond 0.00637 / 0.32 ( 4) SS BOND : angle 1.01023 / 0.51 ( 8) hydrogen bonds : bond 0.03885 / 2.72 ( 1936) hydrogen bonds : angle 4.62322 / 3.35 ( 5616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.9351 (tpp) cc_final: 0.8983 (mmm) REVERT: A 599 MET cc_start: 0.9137 (ttm) cc_final: 0.8877 (ttm) REVERT: A 622 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8935 (ttm) REVERT: A 669 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 930 VAL cc_start: 0.9253 (t) cc_final: 0.8988 (p) REVERT: A 1034 LEU cc_start: 0.9303 (mp) cc_final: 0.8992 (tp) REVERT: B 477 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9266 (mm) REVERT: B 599 MET cc_start: 0.9156 (ttm) cc_final: 0.8759 (ttm) REVERT: B 669 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 951 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9316 (mp) REVERT: B 1034 LEU cc_start: 0.9236 (mp) cc_final: 0.8924 (tp) REVERT: B 1146 GLU cc_start: 0.9490 (mm-30) cc_final: 0.8935 (mp0) REVERT: C 175 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.9337 (mtp) REVERT: C 477 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9291 (mm) REVERT: C 576 MET cc_start: 0.9245 (mmm) cc_final: 0.8879 (mmm) REVERT: C 580 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8920 (mt-10) REVERT: C 599 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8790 (ttm) REVERT: C 660 GLN cc_start: 0.9587 (OUTLIER) cc_final: 0.9107 (mt0) REVERT: C 669 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8317 (tm-30) REVERT: C 951 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9315 (mp) REVERT: C 1034 LEU cc_start: 0.9261 (mp) cc_final: 0.8976 (tp) REVERT: C 1125 GLU cc_start: 0.9391 (tt0) cc_final: 0.9155 (tt0) REVERT: C 1146 GLU cc_start: 0.9502 (mm-30) cc_final: 0.8976 (mp0) REVERT: D 477 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9297 (mm) REVERT: D 599 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8464 (ttp) REVERT: D 669 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 951 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9338 (mp) REVERT: D 1034 LEU cc_start: 0.9295 (mp) cc_final: 0.8950 (tp) REVERT: D 1125 GLU cc_start: 0.9412 (tt0) cc_final: 0.9058 (tm-30) REVERT: D 1146 GLU cc_start: 0.9500 (mm-30) cc_final: 0.8888 (mp0) outliers start: 72 outliers final: 30 residues processed: 266 average time/residue: 0.1661 time to fit residues: 75.0471 Evaluate side-chains 244 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1085 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 244 optimal weight: 0.6980 chunk 273 optimal weight: 0.8980 chunk 348 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 361 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.075660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.056513 restraints weight = 138604.674| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.96 r_work: 0.2729 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 30396 Z= 0.110 Angle : 0.527 11.173 41392 Z= 0.262 Chirality : 0.036 0.157 4788 Planarity : 0.004 0.050 5196 Dihedral : 6.866 89.764 4362 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.37 % Allowed : 11.11 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.14), residues: 3848 helix: 2.53 (0.10), residues: 2488 sheet: -1.07 (0.36), residues: 244 loop : 0.13 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 113 TYR 0.008 0.001 TYR A 227 PHE 0.011 0.001 PHE A 627 TRP 0.010 0.001 TRP B 772 HIS 0.004 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (30392) covalent geometry : angle 0.52677 / 0.26 (41384) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 0.80312 / 0.41 ( 8) hydrogen bonds : bond 0.03428 / 2.40 ( 1936) hydrogen bonds : angle 4.37897 / 3.17 ( 5616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 1.010 Fit side-chains REVERT: A 136 ASP cc_start: 0.9728 (t0) cc_final: 0.9316 (m-30) REVERT: A 576 MET cc_start: 0.9334 (tpp) cc_final: 0.8765 (mmm) REVERT: A 580 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8878 (mt-10) REVERT: A 622 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8875 (ttm) REVERT: A 951 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9280 (mp) REVERT: A 1034 LEU cc_start: 0.9288 (mp) cc_final: 0.8981 (tp) REVERT: A 1125 GLU cc_start: 0.9354 (tt0) cc_final: 0.9135 (tm-30) REVERT: B 136 ASP cc_start: 0.9723 (t0) cc_final: 0.9291 (m-30) REVERT: B 477 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9250 (mm) REVERT: B 1034 LEU cc_start: 0.9223 (mp) cc_final: 0.8890 (tp) REVERT: B 1146 GLU cc_start: 0.9505 (mm-30) cc_final: 0.8993 (mp0) REVERT: C 136 ASP cc_start: 0.9720 (t0) cc_final: 0.9300 (m-30) REVERT: C 477 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9236 (mm) REVERT: C 576 MET cc_start: 0.9243 (mmm) cc_final: 0.8901 (mmm) REVERT: C 580 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8929 (mt-10) REVERT: C 599 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8824 (ttm) REVERT: C 602 LEU cc_start: 0.9785 (OUTLIER) cc_final: 0.9584 (tt) REVERT: C 660 GLN cc_start: 0.9573 (OUTLIER) cc_final: 0.9132 (mt0) REVERT: C 951 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9270 (mp) REVERT: C 1034 LEU cc_start: 0.9245 (mp) cc_final: 0.8917 (tp) REVERT: C 1146 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9013 (mp0) REVERT: D 136 ASP cc_start: 0.9731 (t0) cc_final: 0.9347 (m-30) REVERT: D 477 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9248 (mm) REVERT: D 507 LEU cc_start: 0.9723 (mm) cc_final: 0.9478 (pp) REVERT: D 568 LEU cc_start: 0.9702 (mt) cc_final: 0.9476 (mt) REVERT: D 599 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8488 (ttp) REVERT: D 602 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9572 (tt) REVERT: D 1034 LEU cc_start: 0.9259 (mp) cc_final: 0.8922 (tp) REVERT: D 1146 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9032 (mp0) outliers start: 68 outliers final: 24 residues processed: 325 average time/residue: 0.1599 time to fit residues: 89.1367 Evaluate side-chains 271 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 122 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 362 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.074070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.054633 restraints weight = 141271.754| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.92 r_work: 0.2680 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 30396 Z= 0.269 Angle : 0.617 11.333 41392 Z= 0.306 Chirality : 0.038 0.163 4788 Planarity : 0.004 0.052 5196 Dihedral : 6.737 89.411 4360 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.23 % Allowed : 12.08 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.14), residues: 3848 helix: 2.57 (0.10), residues: 2468 sheet: -1.13 (0.35), residues: 252 loop : 0.10 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 612 TYR 0.009 0.001 TYR C1063 PHE 0.025 0.001 PHE C 373 TRP 0.011 0.001 TRP A1124 HIS 0.010 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.27 (30392) covalent geometry : angle 0.61711 / 0.31 (41384) SS BOND : bond 0.00640 / 0.32 ( 4) SS BOND : angle 0.74660 / 0.37 ( 8) hydrogen bonds : bond 0.03717 / 2.61 ( 1936) hydrogen bonds : angle 4.57416 / 3.30 ( 5616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 219 time to evaluate : 1.130 Fit side-chains REVERT: A 576 MET cc_start: 0.9348 (tpp) cc_final: 0.8912 (mmm) REVERT: A 599 MET cc_start: 0.9098 (ttm) cc_final: 0.8731 (ttm) REVERT: A 622 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8921 (ttm) REVERT: A 951 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9286 (mp) REVERT: A 988 MET cc_start: 0.8961 (ptp) cc_final: 0.8754 (ptp) REVERT: A 1034 LEU cc_start: 0.9307 (mp) cc_final: 0.8951 (tp) REVERT: B 1034 LEU cc_start: 0.9220 (mp) cc_final: 0.8887 (tp) REVERT: B 1146 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9003 (mp0) REVERT: C 477 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9265 (mm) REVERT: C 576 MET cc_start: 0.9334 (mmm) cc_final: 0.8939 (mmm) REVERT: C 580 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8918 (mt-10) REVERT: C 599 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8785 (ttm) REVERT: C 660 GLN cc_start: 0.9603 (OUTLIER) cc_final: 0.9166 (mt0) REVERT: C 951 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9325 (mp) REVERT: C 1034 LEU cc_start: 0.9171 (mp) cc_final: 0.8885 (tp) REVERT: C 1146 GLU cc_start: 0.9541 (mm-30) cc_final: 0.8964 (mp0) REVERT: D 477 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9285 (mm) REVERT: D 576 MET cc_start: 0.9500 (mmm) cc_final: 0.9232 (mmm) REVERT: D 580 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8934 (mp0) REVERT: D 599 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8795 (ttm) REVERT: D 1034 LEU cc_start: 0.9294 (mp) cc_final: 0.8941 (tp) REVERT: D 1125 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.9002 (tm-30) REVERT: D 1146 GLU cc_start: 0.9564 (mm-30) cc_final: 0.8970 (mp0) outliers start: 64 outliers final: 34 residues processed: 267 average time/residue: 0.1641 time to fit residues: 74.8612 Evaluate side-chains 251 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 210 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 328 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 115 optimal weight: 0.0270 chunk 255 optimal weight: 6.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.074736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.055359 restraints weight = 139763.361| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.93 r_work: 0.2702 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30396 Z= 0.172 Angle : 0.568 11.284 41392 Z= 0.282 Chirality : 0.037 0.180 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.682 88.896 4360 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.26 % Allowed : 11.84 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.14), residues: 3848 helix: 2.59 (0.10), residues: 2460 sheet: -1.19 (0.35), residues: 252 loop : 0.04 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 113 TYR 0.008 0.001 TYR C1063 PHE 0.022 0.001 PHE C 373 TRP 0.010 0.001 TRP D 680 HIS 0.012 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (30392) covalent geometry : angle 0.56815 / 0.28 (41384) SS BOND : bond 0.00506 / 0.25 ( 4) SS BOND : angle 0.77682 / 0.39 ( 8) hydrogen bonds : bond 0.03539 / 2.48 ( 1936) hydrogen bonds : angle 4.46082 / 3.22 ( 5616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 1.202 Fit side-chains REVERT: A 576 MET cc_start: 0.9354 (tpp) cc_final: 0.8848 (mmm) REVERT: A 599 MET cc_start: 0.9133 (ttm) cc_final: 0.8766 (ttm) REVERT: A 622 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8875 (ttm) REVERT: A 951 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9274 (mp) REVERT: A 1034 LEU cc_start: 0.9309 (mp) cc_final: 0.8966 (tp) REVERT: B 477 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9291 (mm) REVERT: B 1034 LEU cc_start: 0.9250 (mp) cc_final: 0.8913 (tp) REVERT: B 1146 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9002 (mp0) REVERT: C 136 ASP cc_start: 0.9731 (t0) cc_final: 0.9358 (m-30) REVERT: C 477 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9255 (mm) REVERT: C 576 MET cc_start: 0.9344 (mmm) cc_final: 0.8951 (mmm) REVERT: C 580 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8927 (mt-10) REVERT: C 599 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8754 (ttm) REVERT: C 602 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9569 (tt) REVERT: C 660 GLN cc_start: 0.9609 (OUTLIER) cc_final: 0.9180 (mt0) REVERT: C 951 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9299 (mp) REVERT: C 1034 LEU cc_start: 0.9213 (mp) cc_final: 0.8893 (tp) REVERT: C 1146 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9012 (mp0) REVERT: D 477 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9289 (mm) REVERT: D 599 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8780 (ttm) REVERT: D 602 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9558 (tt) REVERT: D 1034 LEU cc_start: 0.9285 (mp) cc_final: 0.8950 (tp) REVERT: D 1125 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.9013 (tm-30) REVERT: D 1146 GLU cc_start: 0.9535 (mm-30) cc_final: 0.8943 (mp0) outliers start: 65 outliers final: 31 residues processed: 290 average time/residue: 0.1730 time to fit residues: 85.8335 Evaluate side-chains 267 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 307 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 200 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.053252 restraints weight = 142253.393| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.88 r_work: 0.2650 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 30396 Z= 0.320 Angle : 0.668 11.184 41392 Z= 0.331 Chirality : 0.039 0.169 4788 Planarity : 0.004 0.053 5196 Dihedral : 6.637 87.679 4360 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.33 % Allowed : 12.26 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.14), residues: 3848 helix: 2.46 (0.10), residues: 2464 sheet: -1.26 (0.35), residues: 252 loop : -0.01 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 113 TYR 0.011 0.001 TYR A 577 PHE 0.019 0.001 PHE C 373 TRP 0.011 0.001 TRP B1124 HIS 0.014 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.32 (30392) covalent geometry : angle 0.66824 / 0.33 (41384) SS BOND : bond 0.00763 / 0.38 ( 4) SS BOND : angle 0.69344 / 0.35 ( 8) hydrogen bonds : bond 0.03941 / 2.77 ( 1936) hydrogen bonds : angle 4.68398 / 3.39 ( 5616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 576 MET cc_start: 0.9376 (tpp) cc_final: 0.8987 (mmm) REVERT: A 622 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8864 (ttm) REVERT: A 1034 LEU cc_start: 0.9291 (mp) cc_final: 0.8924 (tp) REVERT: B 477 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9297 (mm) REVERT: B 1034 LEU cc_start: 0.9247 (mp) cc_final: 0.8910 (tp) REVERT: B 1146 GLU cc_start: 0.9549 (mm-30) cc_final: 0.8979 (mp0) REVERT: C 477 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9278 (mm) REVERT: C 576 MET cc_start: 0.9331 (mmm) cc_final: 0.8977 (mmm) REVERT: C 580 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8945 (mt-10) REVERT: C 599 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8785 (ttm) REVERT: C 602 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9568 (tt) REVERT: C 660 GLN cc_start: 0.9630 (OUTLIER) cc_final: 0.9201 (mt0) REVERT: C 951 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9301 (mp) REVERT: C 1034 LEU cc_start: 0.9251 (mp) cc_final: 0.8941 (tp) REVERT: C 1146 GLU cc_start: 0.9559 (mm-30) cc_final: 0.8951 (mp0) REVERT: D 599 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8791 (ttm) REVERT: D 1034 LEU cc_start: 0.9327 (mp) cc_final: 0.8964 (tp) REVERT: D 1125 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.9094 (tm-30) REVERT: D 1146 GLU cc_start: 0.9539 (mm-30) cc_final: 0.8949 (mp0) outliers start: 67 outliers final: 36 residues processed: 254 average time/residue: 0.1645 time to fit residues: 71.3745 Evaluate side-chains 248 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1157 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 158 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.074943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055684 restraints weight = 138157.133| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.95 r_work: 0.2716 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30396 Z= 0.130 Angle : 0.581 12.281 41392 Z= 0.282 Chirality : 0.037 0.187 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.625 89.229 4360 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.74 % Allowed : 12.81 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.14), residues: 3848 helix: 2.51 (0.10), residues: 2460 sheet: -1.23 (0.35), residues: 252 loop : -0.00 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1138 TYR 0.008 0.001 TYR D1063 PHE 0.019 0.001 PHE C 373 TRP 0.010 0.001 TRP B1058 HIS 0.012 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (30392) covalent geometry : angle 0.58106 / 0.28 (41384) SS BOND : bond 0.00426 / 0.21 ( 4) SS BOND : angle 0.76711 / 0.39 ( 8) hydrogen bonds : bond 0.03489 / 2.44 ( 1936) hydrogen bonds : angle 4.45330 / 3.23 ( 5616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9359 (tpp) cc_final: 0.8853 (mmm) REVERT: A 622 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8836 (ttm) REVERT: A 1034 LEU cc_start: 0.9311 (mp) cc_final: 0.8989 (tp) REVERT: B 477 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9229 (mm) REVERT: B 599 MET cc_start: 0.9112 (ttm) cc_final: 0.8876 (ttm) REVERT: B 951 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9246 (mp) REVERT: B 1034 LEU cc_start: 0.9206 (mp) cc_final: 0.8869 (tp) REVERT: B 1146 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9042 (mp0) REVERT: C 477 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9242 (mm) REVERT: C 599 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8598 (ttm) REVERT: C 602 LEU cc_start: 0.9782 (OUTLIER) cc_final: 0.9573 (tt) REVERT: C 951 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9262 (mp) REVERT: C 1034 LEU cc_start: 0.9227 (mp) cc_final: 0.8897 (tp) REVERT: D 580 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8947 (mp0) REVERT: D 599 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8864 (ttm) REVERT: D 1034 LEU cc_start: 0.9309 (mp) cc_final: 0.8982 (tp) REVERT: D 1125 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.9047 (tm-30) outliers start: 50 outliers final: 31 residues processed: 282 average time/residue: 0.1812 time to fit residues: 86.8132 Evaluate side-chains 271 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 313 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 123 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 339 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.074020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054571 restraints weight = 140724.695| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.92 r_work: 0.2684 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30396 Z= 0.231 Angle : 0.628 11.869 41392 Z= 0.306 Chirality : 0.038 0.194 4788 Planarity : 0.004 0.057 5196 Dihedral : 6.557 89.999 4360 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.64 % Allowed : 13.30 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.14), residues: 3848 helix: 2.50 (0.10), residues: 2468 sheet: -1.22 (0.35), residues: 252 loop : 0.01 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 113 TYR 0.010 0.001 TYR C1063 PHE 0.016 0.001 PHE C 373 TRP 0.009 0.001 TRP B1124 HIS 0.009 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 (30392) covalent geometry : angle 0.62785 / 0.31 (41384) SS BOND : bond 0.00606 / 0.30 ( 4) SS BOND : angle 0.65033 / 0.33 ( 8) hydrogen bonds : bond 0.03648 / 2.56 ( 1936) hydrogen bonds : angle 4.53382 / 3.28 ( 5616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9310 (tpp) cc_final: 0.8846 (mmm) REVERT: A 599 MET cc_start: 0.9160 (ttm) cc_final: 0.8889 (ttm) REVERT: A 622 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8846 (ttm) REVERT: A 1034 LEU cc_start: 0.9311 (mp) cc_final: 0.8962 (tp) REVERT: B 477 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9238 (mm) REVERT: B 599 MET cc_start: 0.9129 (ttm) cc_final: 0.8860 (ttm) REVERT: B 951 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9271 (mp) REVERT: B 1034 LEU cc_start: 0.9247 (mp) cc_final: 0.8894 (tp) REVERT: B 1146 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9012 (mp0) REVERT: C 477 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9261 (mm) REVERT: C 580 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8886 (mp0) REVERT: C 599 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8740 (ttm) REVERT: C 602 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9560 (tt) REVERT: C 951 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9292 (mp) REVERT: C 1034 LEU cc_start: 0.9244 (mp) cc_final: 0.8914 (tp) REVERT: C 1146 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9016 (mp0) REVERT: D 580 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8942 (mp0) REVERT: D 599 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8853 (ttm) REVERT: D 1034 LEU cc_start: 0.9324 (mp) cc_final: 0.8961 (tp) REVERT: D 1125 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9110 (tm-30) REVERT: D 1146 GLU cc_start: 0.9560 (mm-30) cc_final: 0.8992 (mp0) outliers start: 47 outliers final: 33 residues processed: 260 average time/residue: 0.1796 time to fit residues: 79.5314 Evaluate side-chains 266 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 104 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 201 optimal weight: 40.0000 chunk 281 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 384 optimal weight: 0.1980 chunk 137 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.075847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056823 restraints weight = 137911.988| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.93 r_work: 0.2742 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30396 Z= 0.113 Angle : 0.587 12.357 41392 Z= 0.281 Chirality : 0.037 0.259 4788 Planarity : 0.004 0.051 5196 Dihedral : 6.472 89.684 4360 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.39 % Allowed : 13.41 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.14), residues: 3848 helix: 2.44 (0.10), residues: 2488 sheet: -1.21 (0.35), residues: 252 loop : -0.05 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 113 TYR 0.007 0.001 TYR D1063 PHE 0.017 0.001 PHE C 373 TRP 0.011 0.001 TRP B 772 HIS 0.003 0.001 HIS B1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (30392) covalent geometry : angle 0.58702 / 0.28 (41384) SS BOND : bond 0.00304 / 0.15 ( 4) SS BOND : angle 0.68291 / 0.35 ( 8) hydrogen bonds : bond 0.03304 / 2.30 ( 1936) hydrogen bonds : angle 4.38271 / 3.18 ( 5616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6355.39 seconds wall clock time: 109 minutes 57.52 seconds (6597.52 seconds total)